tests/testthat/test-neargenes.R

In ELMER: Inferring Regulatory Element Landscapes and Transcription Factor Networks Using Cancer Methylomes

context("Get GetNearGenes")

test_that("It maps correctly to hg38", {
  tssAnnot <- getTSS(genome = "hg38")
  geneAnnot <- tssAnnot

  probe <- getInfiniumAnnotation(genome = "hg19")["cg18108049"]

  NearbyGenes <- getRegionNearGenes(TRange = probe,
                                    geneAnnot = geneAnnot,
                                    numFlankingGenes = 4)
  
  expect_equal(NearbyGenes[NearbyGenes$Side == "L2",]$GeneID , "ENSG00000184908")
  expect_equal(NearbyGenes[NearbyGenes$Side == "L1",]$GeneID, "ENSG00000185519")
  expect_equal(NearbyGenes[NearbyGenes$Side == "L2",]$Symbol, "CLCNKB")
  expect_equal(NearbyGenes[NearbyGenes$Side == "L1",]$Symbol, "FAM131C")
  expect_equal(NearbyGenes[NearbyGenes$Side == "R1",]$GeneID, "ENSG00000142627")
  expect_equal(NearbyGenes[NearbyGenes$Side == "R1",]$Symbol, "EPHA2")
  
  NearbyGenes <- GetNearGenes(numFlankingGenes = 4,
                              geneAnnot = geneAnnot,
                              TRange = probe)
  expect_equal(NearbyGenes[NearbyGenes$Side == "L2",]$GeneID, "ENSG00000184908")
  expect_equal(NearbyGenes[NearbyGenes$Side == "L1",]$GeneID, "ENSG00000185519")
  expect_equal(NearbyGenes[NearbyGenes$Side == "L2",]$Symbol, "CLCNKB")
  expect_equal(NearbyGenes[NearbyGenes$Side == "L1",]$Symbol, "FAM131C")
  expect_equal(NearbyGenes[NearbyGenes$Side == "R1",]$GeneID, "ENSG00000142627")
  expect_equal(NearbyGenes[NearbyGenes$Side == "R1",]$Symbol, "EPHA2")
})


test_that("It maps correctly to hg38 if more than one region", {
  tssAnnot <- getTSS(genome = "hg38")
  geneAnnot <- tssAnnot
  probe <- getInfiniumAnnotation(genome = "hg19")[c("cg18108049","cg14008030","cg00381604","cg15254640","cg08417382")] 
  
  NearbyGenes <- getRegionNearGenes(TRange = probe,
                                    geneAnnot = geneAnnot,
                                    numFlankingGenes = 4)
  
  expect_equal(NearbyGenes[NearbyGenes$Side == "L2" & NearbyGenes$ID == "cg18108049",]$GeneID , "ENSG00000184908")
  expect_equal(NearbyGenes[NearbyGenes$Side == "L1"  & NearbyGenes$ID == "cg18108049",]$GeneID, "ENSG00000185519")
  expect_equal(NearbyGenes[NearbyGenes$Side == "L2" & NearbyGenes$ID == "cg18108049",]$Symbol, "CLCNKB")
  expect_equal(NearbyGenes[NearbyGenes$Side == "L1" & NearbyGenes$ID == "cg18108049",]$Symbol, "FAM131C")
  expect_equal(NearbyGenes[NearbyGenes$Side == "R1" & NearbyGenes$ID == "cg18108049",]$GeneID, "ENSG00000142627")
  expect_equal(NearbyGenes[NearbyGenes$Side == "R1" & NearbyGenes$ID == "cg18108049",]$Symbol, "EPHA2")
  
  NearbyGenes <- GetNearGenes(numFlankingGenes = 20,
                              geneAnnot = geneAnnot,
                              TRange = probe)
  expect_equal(NearbyGenes[NearbyGenes$Side == "L2" & NearbyGenes$ID == "cg18108049",]$GeneID, "ENSG00000184908")
  expect_equal(NearbyGenes[NearbyGenes$Side == "L1" & NearbyGenes$ID == "cg18108049",]$GeneID, "ENSG00000185519")
  expect_equal(NearbyGenes[NearbyGenes$Side == "L2" & NearbyGenes$ID == "cg18108049",]$Symbol, "CLCNKB")
  expect_equal(NearbyGenes[NearbyGenes$Side == "L1" & NearbyGenes$ID == "cg18108049",]$Symbol, "FAM131C")
  expect_equal(NearbyGenes[NearbyGenes$Side == "R1" & NearbyGenes$ID == "cg18108049",]$GeneID, "ENSG00000142627")
  expect_equal(NearbyGenes[NearbyGenes$Side == "R1" & NearbyGenes$ID == "cg18108049",]$Symbol, "EPHA2")
})

test_that("It maps correctly to hg19", {
  tssAnnot <- getTSS(genome = "hg19")
  geneAnnot <- tssAnnot
  probe <- getInfiniumAnnotation(genome = "hg19")["cg18108049"]
  
  # chr1:16010827:16062808
  # chr1:16058489:16058489
  NearbyGenes <- getRegionNearGenes(TRange = probe,
                                    geneAnnot = geneAnnot,
                                    numFlankingGenes = 30)
  
  expect_true(all(c("SLC25A34","RSC1A1","AGMAT","DDI2","PLEKHM2") %in% NearbyGenes$Symbol))
})